Contacts of the helix formed by residues 358 - 375 (chain B) in PDB entry 4H1S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B ASP* 3.4 11.4 - - - +
352B SER* 3.9 16.4 - - - -
353B CYS* 2.1 53.6 - - - -
356B ARG 3.2 0.6 + - - -
357B GLU* 1.3 74.4 - - - +
359B ASN* 1.3 59.0 + - - +
361B GLY* 3.0 31.9 + - - -
362B ASN* 3.2 13.2 + - - -
451B GLN* 3.0 18.7 + - - +
542B VAL* 4.4 4.0 - - - -
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Residues in contact with ASN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A VAL* 3.7 18.1 - - + +
344B VAL* 3.6 10.1 - - - +
345B TYR 2.9 21.6 + - - -
346B LEU* 4.2 1.5 - - - +
347B ASP* 2.9 32.8 + - - +
358B CYS* 1.3 69.3 - - - +
360B MET* 1.3 61.5 + - - +
362B ASN* 3.8 8.1 - - - +
363B LEU* 3.0 22.2 + - - +
540B PRO* 3.0 47.8 + - - +
541B ALA 3.9 13.2 - - - -
542B VAL* 4.0 5.2 - - - +
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Residues in contact with MET 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.6 33.9 - - + +
347B ASP 3.2 22.8 + - - +
348B GLY* 3.7 2.5 - - - -
358B CYS* 3.2 0.8 - - - -
359B ASN* 1.3 80.4 + - - +
361B GLY* 1.3 60.6 + - - +
363B LEU* 3.3 23.4 + - - +
364B ILE* 3.0 37.9 + - + +
394B ILE* 3.8 22.2 - - + -
396B SER 3.4 22.7 - - - +
398B ILE* 3.8 13.7 - - + +
411B LEU* 6.2 2.2 - - - -
414B VAL* 3.9 20.0 - - + -
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Residues in contact with GLY 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B CYS* 3.0 12.9 + - - -
360B MET* 1.3 76.4 - - - +
362B ASN* 1.3 59.9 + - - +
364B ILE* 3.3 1.7 + - - +
365B CYS* 2.9 31.6 + - - +
389B LEU* 4.1 5.4 - - - +
394B ILE* 3.6 23.5 - - - +
451B GLN* 3.9 18.2 - - - -
452B VAL 5.1 0.2 - - - -
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Residues in contact with ASN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLU* 2.8 37.0 + - - +
358B CYS 3.2 10.6 + - - +
359B ASN* 3.7 7.8 - - - +
360B MET 3.3 0.2 - - - -
361B GLY* 1.3 76.7 - - - +
363B LEU* 1.3 55.5 + - - +
365B CYS 3.4 0.3 + - - -
366B ASP* 2.8 39.4 + - - +
451B GLN* 4.5 3.3 - - - +
452B VAL 3.6 7.1 + - - +
540B PRO* 4.8 4.3 - - + -
541B ALA 2.9 25.1 + - - +
542B VAL* 4.1 0.6 - - - +
543B GLU* 4.2 0.8 + - - +
545B ARG* 3.2 43.0 + - - +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.3 12.1 - - + -
359B ASN 3.0 14.7 + - - +
360B MET* 3.4 29.4 - - - +
362B ASN* 1.3 76.1 - - - +
364B ILE* 1.3 60.8 + - + +
366B ASP* 3.8 4.0 - - - +
367B ALA* 2.9 28.8 + - - +
398B ILE* 6.4 0.2 - - + -
411B LEU* 6.3 0.4 - - + -
528B VAL* 4.7 16.2 - - + -
531B TYR* 3.7 29.2 - - + -
532B ILE* 4.8 5.6 - - + -
538B ILE* 3.9 33.4 - - + -
540B PRO* 3.9 17.4 - - + +
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B MET* 3.0 39.3 + - + +
361B GLY 3.3 0.2 + - - -
363B LEU* 1.3 78.8 - - + +
365B CYS* 1.3 57.0 + - - +
367B ALA* 3.2 5.8 + - - +
368B MET* 2.8 35.8 + - - +
389B LEU* 3.7 19.7 - - + -
394B ILE* 4.2 17.5 - - + -
414B VAL* 4.3 6.1 - - + -
415B LEU* 3.9 24.9 - - + -
421B PHE* 3.7 28.7 - - + -
528B VAL* 4.2 18.4 - - + -
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Residues in contact with CYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLY 2.9 17.1 + - - +
362B ASN 4.0 1.3 - - - +
364B ILE* 1.3 76.7 - - - +
366B ASP* 1.3 65.2 + - - +
368B MET* 3.2 2.6 + - - +
369B ILE* 3.0 29.0 + - - +
387B CYS* 2.0 57.8 - - + -
388B ILE 4.0 1.1 - - - -
389B LEU* 4.0 19.1 - - - -
451B GLN 4.1 0.2 - - - -
452B VAL* 3.7 27.6 - - - +
453B GLY* 3.9 2.2 - - - +
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Residues in contact with ASP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A TYR* 4.7 1.7 + - - -
362B ASN* 2.8 24.2 + - - +
363B LEU* 4.0 4.8 - - - +
365B CYS* 1.3 72.6 - - - +
367B ALA* 1.3 58.4 + - - +
369B ILE* 3.5 9.0 + - - +
370B ASN* 2.9 30.8 + - - +
453B GLY* 4.5 4.2 - - - -
531B TYR* 4.2 16.1 - - - +
540B PRO* 6.0 1.2 - - - +
543B GLU* 5.3 0.3 - - - +
545B ARG* 2.7 39.2 + - - -
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU 2.9 18.8 + - - +
364B ILE* 3.6 6.7 - - - +
366B ASP* 1.3 74.8 - - - +
368B MET* 1.3 59.8 + - - +
370B ASN* 3.9 0.2 - - - +
371B ASN* 2.9 32.9 + - - +
527B VAL* 3.5 4.2 - - + +
528B VAL* 4.4 19.3 - - + -
531B TYR* 3.5 40.7 - - + +
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Residues in contact with MET 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE* 2.8 30.6 + - - +
365B CYS* 3.5 8.3 - - - +
367B ALA* 1.3 75.4 - - - +
369B ILE* 1.3 63.0 + - - +
371B ASN* 4.1 1.7 + - - +
372B ASN* 3.2 17.2 + - - +
387B CYS* 3.4 23.8 - - - -
388B ILE 4.3 1.6 - - - +
389B LEU* 4.7 7.4 - - - -
421B PHE* 3.4 49.4 - - + -
496B ILE* 3.4 31.0 - - + +
497B LEU* 3.5 38.1 - - - +
498B PRO 4.3 0.7 - - - -
527B VAL* 4.1 7.4 - - - -
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Residues in contact with ILE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A TYR* 4.3 12.6 - - + +
365B CYS 3.0 20.4 + - - +
366B ASP* 3.8 9.0 - - - +
368B MET* 1.3 76.4 - - - +
370B ASN* 1.3 56.9 + - - +
372B ASN* 3.3 4.8 + - - +
373B LEU* 2.9 42.6 + - + +
384B VAL* 3.6 20.4 - - - +
385B SER* 3.3 31.9 - - - +
387B CYS* 3.8 22.9 - - + -
453B GLY* 4.2 11.7 - - - -
454B GLY 4.6 0.9 - - - +
496B ILE* 3.9 11.9 - - + -
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Residues in contact with ASN 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A MET* 5.4 5.9 - - - +
537A VAL 4.9 3.6 + - - -
539A TYR* 3.1 33.0 + - - +
366B ASP 2.9 19.3 + - - +
367B ALA 3.9 0.2 - - - +
369B ILE* 1.3 73.8 - - - +
371B ASN* 1.3 67.2 + - - +
373B LEU* 3.3 4.4 + - - +
374B ARG* 2.9 63.6 + - - +
531B TYR* 3.7 31.1 - - + -
535B MET* 5.5 0.4 - - - -
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Residues in contact with ASN 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B ALA 2.9 18.1 + - - +
368B MET 4.1 2.2 + - - +
370B ASN* 1.3 79.1 + - - +
372B ASN* 1.3 68.8 + - - +
374B ARG* 3.4 2.4 + - - -
375B HIS* 3.0 48.1 + - - +
496B ILE* 6.2 0.6 - - - +
522B ASP* 2.7 33.0 + - - +
527B VAL* 3.6 29.2 - - + +
530B THR* 4.3 11.5 + - - +
531B TYR* 5.3 1.7 - - + -
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Residues in contact with ASN 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B MET 3.2 17.0 + - - +
369B ILE* 3.8 4.2 + - - +
371B ASN* 1.3 86.7 - - - +
373B LEU* 1.3 66.4 + - - +
375B HIS 3.3 23.6 + - - +
381B TRP* 3.0 30.5 + - - +
382B ASN* 5.3 3.3 - - - +
384B VAL* 3.8 15.8 + - - +
423B LEU* 3.3 31.2 - - - +
496B ILE* 3.9 12.1 - - + -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ILE* 3.9 12.8 - - + +
537A VAL* 4.5 13.3 - - + +
539A TYR* 3.6 52.7 - - + -
369B ILE* 2.9 26.6 + - + +
370B ASN* 3.3 5.6 + - - +
372B ASN* 1.3 80.1 - - - +
374B ARG* 1.3 60.2 + - + +
375B HIS 3.7 1.0 + - - +
382B ASN* 3.3 41.9 - - - +
383B HIS* 3.8 4.3 - - - +
384B VAL 3.6 23.6 - - - +
385B SER* 5.7 1.3 - - - -
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Residues in contact with ARG 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A LYS 3.7 8.3 + - - -
535A MET* 2.9 44.7 + - - +
536A LYS* 3.5 19.7 - - + +
537A VAL* 3.9 26.7 - - + +
370B ASN* 2.9 47.2 + - - +
371B ASN* 3.8 1.1 - - - +
373B LEU* 1.3 76.8 - - + +
375B HIS* 1.3 100.8 + - + +
531B TYR* 5.6 0.4 - - - -
534B LYS* 4.7 21.0 - - - +
535B MET* 4.8 4.4 - - - -
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Residues in contact with HIS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ASN* 3.0 42.0 + - - +
372B ASN* 3.3 18.5 + - - +
373B LEU 4.8 1.0 - - - +
374B ARG* 1.3 120.7 - - + +
379B MET* 5.5 7.4 - - - +
382B ASN* 6.2 0.2 - - - +
522B ASP* 4.8 5.4 - - - +
530B THR* 5.7 4.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il